Dataset Information

Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform.

ABSTRACT: The second virial coefficient, B2, measures a protein solution's deviation from ideal behavior. It is widely used to predict or explain solubility, crystallization condition, aggregation propensity, and critical temperature for liquid-liquid phase separation. B2 is determined by the interaction energy between two protein molecules and, specifically, by the integration of the Mayer f-function in the relative configurational space (translation and rotation) of the two molecules. Simple theoretical models, such as one attributed to Derjaguin, Landau, Verwey, and Overbeek (DLVO), can fit the dependence of B2 on salt concentrations. However, model parameters derived often are physically unrealistic and hardly transferable from protein to protein. Previous B2 calculations incorporating atomistic details were done with limited sampling in the configurational space, due to enormous computational cost. Our FMAP method, based on fast Fourier transform, can considerably accelerate such calculations, and here we adapt it to calculate B2 values for proteins represented at the atomic level in implicit solvent. After tuning of a single parameter in the energy function, FMAPB2 predicts well the B2 values for lysozyme and other proteins over wide ranges of solvent conditions (salt concentration, pH, and temperature). The method is available as a web server at http://pipe.rcc.fsu.edu/fmapb2 .

SUBMITTER: Qin S

PROVIDER: S-EPMC7032052 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform.

Qin Sanbo S Zhou Huan-Xiang HX

The journal of physical chemistry. B 20190919 39

The second virial coefficient, B2, measures a protein solution's deviation from ideal behavior. It is widely used to predict or explain solubility, crystallization condition, aggregation propensity, and critical temperature for liquid-liquid phase separation. B2 is determined by the interaction energy between two protein molecules and, specifically, by the integration of the Mayer f-function in the relative configurational space (translation and rotatio ...[more]

PMID: 31490691

Similar Datasets

Project description:BackgroundT-wave alternans (TWA) has been associated with increased vulnerability to ventricular tachyarrhythmias and sudden cardiac death. However, both random (white) noise and (patho)physiologic processes (ie, premature ventricular contractions and heart and respiration rates) may hamper TWA estimation and therefore lessen its clinical utility for risk stratification.ObjectiveTo investigate the effect of random noise and certain (patho)physiologic processes on the estimation of TWA by using the fast Fourier transform method and to develop methods to overcome these potential sources of error.MethodsWe used a combination of human electrocardiogram data and computer simulations to assess the effects of a premature ventricular contraction and random and colored noise on the accuracy of TWA estimation.ResultsWe quantitatively demonstrate that replacing a "bad" beat with an odd/even median beat is a more accurate approach than replacing it with the overall average or the overall median beat. We also show that phase resetting may have a significant effect on alternans estimation and that estimation of alternans by using frequencies >0.4922 cycles/beat in a 128-point fast Fourier transform provides the most accurate approach for estimating the alternans when phase resetting is likely to occur. In addition, our data demonstrate that the number of indeterminate TWA tests due to high levels of noise can be reduced when the alternans voltage exceeds a new higher threshold. Furthermore, the amplitude of random noise has a significant effect on alternans estimation and the alternans voltage threshold should be adjusted for noise levels >1.8 μV. Finally, we quantitatively demonstrate that colored noise may lead to a false-positive or a false-negative result. We propose methods to estimate the effect of these (patho)physiologic processes on the alternans estimation in order to determine whether a TWA test is likely to be a true positive or a true negative.ConclusionThis study introduces novel methods to overcome potential sources of error in the estimation of TWA. These methods may improve the utility of TWA either for ambulatory monitoring or for clinical risk stratification for ventricular arrhythmias and sudden cardiac death.

Dataset Information

Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform.

Publications

Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets